References
- M. Karplus and J.A. McCammon, Nat. Struct. Mol. Biol. 9, 646 (2002). doi: 10.1038/nsb0902-646
- B.D. Zoltowski and B.R. Crane, Biochemistry. 47, 7012 (2008). doi: 10.1021/bi8007017
- E. Kim and M. Sheng, Nat. Rev. Neurosci. 5, 771 (2004). doi: 10.1038/nrn1517
- O.A. Olabisi, J.-Y. Zhang, L. VerPlank, N. Zahler, S. DiBartolo, J.F. Heneghan, J.S. Schlöndorff, J.H. Suh, P. Yan and S.L. Alper, Proc. Natl. Acad. Sci. U.S.A. 113, 830 (2016). doi: 10.1073/pnas.1522913113
- T. Jinadasa, E.Z. Szabó, M. Numata and J. Orlowski, J. Biol. Chem. 289, 20879 (2014). doi: 10.1074/jbc.M114.555284
- K. Gunasekaran, B. Ma and R. Nussinov, Proteins Struct., Funct. Bioinf. 57, 433 (2004). doi: 10.1002/prot.20232
- G. Kar, O. Keskin, A. Gursoy and R. Nussinov, Curr. Opin. Pharmacol. 10, 715 (2010). doi: 10.1016/j.coph.2010.09.002
- Y. Xu, M.P. Bhate and A.E. McDermott, Proc. Natl. Acad. Sci. U.S.A. 114, 8788 (2017). doi: 10.1073/pnas.1701330114
- A.P. Kornev and S.S. Taylor, Trends Biochem. Sci. 40, 628 (2015). doi: 10.1016/j.tibs.2015.09.002
- A.M. Ruschak and L.E. Kay, Proc. Natl. Acad. Sci. U.S.A. 109, E3454 (2012). doi: 10.1073/pnas.1213640109
- A.J. Wand, Nat. Struct. Mol. Biol. 8, 926 (2001). doi: 10.1038/nsb1101-926
- A.P. Kornev, Biochem. Soc. Trans. 46, 587 (2018). doi: 10.1042/BST20160144
- D.A. Capdevila, K.A. Edmonds, G.C. Campanello, H. Wu, G. Gonzalez-Gutierrez and D.P. Giedroc, J. Am. Chem. Soc. 140, 9108 (2018). doi: 10.1021/jacs.8b02129
- Y. Naritomi and S. Fuchigami, J. Chem. Phys. 134, 065101 (2011). doi: 10.1063/1.3554380
- S. Kullback and R.A. Leibler, Ann. Math. Stat. 22, 79 (1951). doi: 10.1214/aoms/1177729694
- V. Balasubramanian, J.J. Heckman and A. Maloney, J. High Energy Phys. 2015, 104 (2015). doi: 10.1007/JHEP05(2015)104
- H. Zhou, F. Wang and P. Tao, J. Chem. Theory Comput. ASAP (2018) doi:10.1021/acs.jctc.8b00652.
- H. Zhou, Z. Dong and P. Tao, J. Comput. Chem. 39, 1481 (2018). doi: 10.1002/jcc.25218
- D.J. Galas, G. Dewey, J. Kunert-Graf and N.A. Sakhanenko, Axioms. 6, 8 (2017). doi: 10.3390/axioms6020008
- N.R. Maddux, A.L. Daniels and T.W. Randolph, J. Pharm. Sci. 106, 1239 (2017). doi: 10.1016/j.xphs.2017.01.030
- B. Chakrabarty and N. Parekh, Nucleic Acids Res. 44, W375 (2016). doi: 10.1093/nar/gkw383
- R. Heffernan, Y. Yang, K. Paliwal, and Y. Zhou, Bioinformatics 33, 2842 (2017). doi: 10.1093/bioinformatics/btx218
- S. Wang, S. Sun, Z. Li, R. Zhang and J. Xu, PLoS Comp. Biol. 13, e1005324 (2017). doi: 10.1371/journal.pcbi.1005324
- E. Fuglebakk, S.P. Tiwari and N. Reuter, Biochim. Biophys. Acta Gen. Subj. 1850, 911 (2015). doi: 10.1016/j.bbagen.2014.09.021
- P. Guzel and O. Kurkcuoglu, Biochim. Biophys. Acta Gen. Subj. 1861, 3131 (2017). doi: 10.1016/j.bbagen.2017.09.005
- J. Eargle and Z. Luthey-Schulten, Bioinformatics 28, 3000 (2012). doi: 10.1093/bioinformatics/bts546
- V.A. Feher, J.D. Durrant, A.T. Van Wart and R.E. Amaro, Curr. Opin. Struct. Biol. 25, 98 (2014). doi: 10.1016/j.sbi.2014.02.004
- Y. Kong and M. Karplus, Proteins: Struct. Funct. Bioinf. 74, 145 (2009). doi: 10.1002/prot.22139
- Z.N. Gerek and S.B. Ozkan, PLoS Comp. Biol. 7, e1002154 (2011). doi: 10.1371/journal.pcbi.1002154
- H.M. Berman, T.N. Bhat, P.E. Bourne, Z. Feng, G. Gilliland, H. Weissig and J. Westbrook, Nat. Struct. Mol. Biol. 7, 957 (2000). doi: 10.1038/80734
- W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey and M.L. Klein, J. Chem. Phys. 79, 926 (1983). doi: 10.1063/1.445869
- U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee and L.G. Pedersen, J. Chem. Phys. 103, 8577 (1995). doi: 10.1063/1.470117
- B.R. Brooks, C.L. Brooks, A.D. MacKerell, L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels and S. Boresch, J. Comput. Chem. 30, 1545 (2009). doi: 10.1002/jcc.21287
- P. Eastman and V. Pande, Comput. Sci. Eng. 12, 34 (2010). doi: 10.1109/MCSE.2010.27
- E.W. Dijkstra, Numer. Math. 1, 269 (1959). doi: 10.1007/BF01386390
- M. Girvan and M.E.J. Newman, Proc. Natl. Acad. Sci. U.S.A. 99, 7821 (2002). doi: 10.1073/pnas.122653799
- B.W. Kernighan and S. Lin, Bell Syst. Tech. J. 49, 291 (1970). doi: 10.1002/j.1538-7305.1970.tb01770.x
- J. Zhang, P.J. Sapienza, H. Ke, A. Chang, S.R. Hengel, H. Wang, G.N. Phillips Jr and A.L. Lee, Biochemistry. 49, 9280 (2010). doi: 10.1021/bi101131f
- R. Kalescky, H. Zhou, J. Liu and P. Tao, PLoS Comp. Biol. 12, e1004893 (2016). doi: 10.1371/journal.pcbi.1004893
- E.J. Fuentes, C.J. Der and A.L. Lee, J. Mol. Biol. 335, 1105 (2004). doi: 10.1016/j.jmb.2003.11.010
- F. Raimondi, A. Felline, M. Seeber, S. Mariani and F. Fanelli, J. Chem. Theory Comput. 9, 2504 (2013). doi: 10.1021/ct400096f
- A. del Sol, C.J. Tsai, B. Ma and R. Nussinov, Structure. 17, 1042 (2009). doi: 10.1016/j.str.2009.06.008
- A. Sethi, J. Eargle, A.A. Black and Z. Luthey-Schulten, Proc. Natl. Acad. Sci. U.S.A. 106, 6620 (2009). doi: 10.1073/pnas.0810961106